I keep all my patterns stored on my computer, and backed up in a external hard drive. For the patterns I have purchased they are kept in a large folder as well as on the computer. They are put into several catagories, portrait animals, native american, religion and so on. Each folder sometimes has sub folders. Then when needed I print one out. For larger patterns like intarsia, I scan each section of the pattern into my computer, then print each piece out and put together. The originals never get used.
I keep a "to cut" stack in my shop which rarely seems to get any smaller.